In genome-scale datasets, Gene Ontology (GO) enrichment is a common analysis to highlight functions over-represented or under-represented in a subset of differentially expressed genes to elucidate the biological significance of the results. However, despite the diversity of existing tools to analyze GO enrichment, it is often difficult to integrate results in an article figure with sufficient clarity. This is partly due to the high number and to the redundancy of the enriched GO terms, especially when looking at large sets of differentially expressed genes. Here, we provide a simple method to plot representative enriched GO terms. The list of representative enriched GO terms is obtained using existing tools Panther and REVIGO and results are represented in different plots generated from a homemade R script and the ggplot2 R package. The generated plots are publication-quality figures. The diversity of represented parameters makes the plots highly informative (number of genes associated with the enriched GO terms, fold enrichment and level of statistical significance). Comparison of GO enrichment between different lists of genes in a single plot is possible. As proof of concept, we performed this analysis on an Arabidopsis heat responsive transcriptome dataset recently published. Bio-protocol is an online peer-reviewed protocol journal. Its mission is to make life science research more efficient and reproducible by curating and hosting high quality, free access protocols.

Soil seed banks play a critical role in the maintenance of wetland plant communities and contribute to revegetation following disturbances. Analysis of the seed bank can therefore inform restoration planning and management. Emergence from seed banks may vary in response to hydrologic conditions and sediment disturbances. To assess the community-level impact of exotic Ludwigia hexapetala on soil seed banks, we compared differences in species composition of standing vegetation among invaded and non-invaded wetlands and the degree of similarity between vegetation and soil seed banks in northern California. To determine potential seed bank recruitment of L. hexapetala and associated plant species, we conducted a seedling emergence assay in response to inundation regime (drawdown vs. flooded) and sediment depth (surface vs. buried). Plant species richness, evenness, and Shannon’s H’ diversity were substantially lower in standing vegetation at L. hexapetala invaded sites as compared to non-invaded sites. Over 12 months, 69 plant taxa germinated from the seed banks, including L. hexapetala and several other exotic taxa. Seedling density varied among sites, being the highest (10,500 seedlings m⁻²) in surface sediments from non-invaded sites subjected to drawdown treatments. These results signal the need for invasive plant management strategies to deplete undesirable seed banks for restoration success.